Young Heroes
by MythMaker258
Summary: Sent to a new world by a misguided wish, Shirou Emiya finds himself in a world full of actual superheroes. Taken in by a kind old sorcerer, what will Shirou do? Will he work tirelessly to get back to his world and Sakura? Or will he finally achieve his dream? (Heaven's Feel route Shirou)
1. Chapter 1

**Hi, everyone! So I recently made a deal with myself that I'd create a crossover fic involving the ending of each route of Fate/Stay Night: Fate, Unlimited Blade Works, and Heaven's Feel. This will be from the end of Heaven's Feel and I hope you enjoy it. It's something that just came to me and I've been meaning to write a Fate/Stay Night crossover with Young Justice. I hope you all enjoy.**

 **Now, let's start.**

A young boy walked into the cavern, only to be met by a bright red light in the center. A massive pillar of flesh and shadows emitted said light, illuminating the entire thing. The boy scanned around, searching for something, until he found it. Two girls, one wielding a sword of light, the other surrounded by giants of darkness. The two fought, evenly matched, with an infinite army of shadows being created only to be struck down by the girl with the jeweled sword. Suddenly, there's an enormous flash of light, blinding all in the cavern.

When sight returned to the boy, he scrambled to the girls, on all fours. The cavern trembles, as one of the girls scream "Nee-san!"

The boy desperately shouted one of the girls name, panting from the strain of his injuries. He finally makes it to the girls, standing up, but finding a horrid sight.

"Tohsaka."

As the ground shakes, the boy is met with the sight as one of the girls, dressed in red and wearing pig tails, was lying face down, blood spilling out onto the ground. The beauty looked like a flower, but had fallen from its stem.

"…Senpai…."

A soft voice calls out and standing near the bloodied body, the other girl stood looking horrified. The other girl was dressed in shadow, her unnatural white hair covered in blood and red eyes leaking tears. Physical shadows danced around her, moving around her body like lightning.

"Sakura."

"…I killed her," Sakura said, horrified and voice trembling.. "Nee-san cared about me, but I killed her."

Her body was covered in both the blood of Tohsaka and the shadows, which connects her to some dark god. She looks at herself in self-hate, cursing everything with all her might.

"I was stupid. I'm sorry. I'm sorry. There's nothing but pain. You always told me not to lose, but I was too stupid to understand. Senpai believed in me, but I just kept betraying him!"

The shadow surged as she continued talking, wrapping around her body.

"….No… I have to stop… But I can't go back! No, no, I don't want this!"

She refuses it, refusing the shadows and its dark god master. She hates it, hates herself, trying to do the only thing she can, kill herself. But she can't, the shadow won't let her, protecting her from the deed. Sakura is being ripped apart by her own sanity and the dark god's wishes.

The boy thinks back, back to when he had a chance of stopping this tragedy. But instead of helping her, the boy was scared, scolding the girl, causing this disaster.

Running past the memories, the boy runs to the blood-soaked girl on the ground. She was still breathing. The boy let out a sigh of relief. It's too early to give up.

"Right, she's not dead," the boy assures her. "She can be saved. No, she has to be saved. We have to save her. Right, Sakura?"

Light and hope returns to Sakura's eyes, releasing a sigh of relief. But the shadow, sensing an opening, tries to take her over once again.

Sakura screams in pain and fear. "No! Run, Senpai!"

She desperately tries to control herself as the shadows surge, coming forth to strike the injured girl and the less injured boy. The boy covers the girl with his body, letting the shadows whip his back. Gasping in pain, the boy can tell the shadows were forced to miss, praising Sakura for her interference.

Sakura gasps, horrified that she caused the boy pain. "No, Senpai! I, I…."

The shadows around her begin swallowing her, trying to protect its host. The boy curses Angra Mainyu, the dark god who used Sakura like a tool, just to be reborn into this world.

"I know," the boy calmly speaks, shrugging off the pain. His wounds disappear, only to be replaced with swords. "It's that kid's fault for not giving up. He's throwing a tantrum because he doesn't want you taken away." The boy struggles to stand, eventually doing so. "Hold on. I'll smack him and get him off of you."

With that promise, the boy begins walking towards Sakura.

The struggling girl staggers back, fearful once again, but not for her sake. "No!" she begged. "Please stop, Senpai!"

But as she desperately begged for the boy to be safe, the shadows strike again, grazing his cheek and only missing due to Sakura's desperation, avoiding decapitating the boy completely. Sakura pants, desperately trying to control it, but failing, as more shadows begin to appear around her. The white haired girl begins crying, but not for herself, but of frustration for not being able to do this.

"…No, Senpai," the girl cries. "I can't suppress it. Nee-san taught me, but I'm going to lose. …I wasn't strong. I'm a coward, a wimp, and a terrible person."

The boy ignores the girl's rant of self-hate and pleas to take safety, as another shadow lance strikes his cheek.

The girl cries more, as her beloved senpai is struck once again by her uncontrollable powers. "No, why are you coming, Senpai?! I'll kill you if you come any closer!"

This wasn't a threat, but simply stating a fact, a fact she's unable to change and causes her own self-hatred. This, this was hell. Her own existence was bane, killing and ripping apart the ones she cares about. But the boy selfishly takes another step, only wishing to do one thing. He puts a gentle right hand on his left shoulder, grabbing the holy shroud sealing his power, but also keeping away his death.

"Why?" Sakura screams in desperation, voice breaking. "Run! Please run, Senpai! Please take Nee-san and run! You can forget about me! I'll, I'll die here! I can die by myself! I don't want you to see me like this!"

The shadows coil tighter with each step the boy takes; the boy's advance was hurting Sakura on both a physical and mental level.

"Why aren't you listening to me?!" Sakura says, trying to understand what's happening. "I won't hold back if you're going to come any closer. I'll kill you before you kill me!"

Again, this is not a threat nor is it a promise. Simply another desperate fact that cannot be changed.

The boy merely smiles at his silly kouhai. "I don't need to explain. I'm going to get you out of here and save Tohsaka. That's what I said, right?"

Sakura's face turned from pained and afraid to merely concerned. "A-are you still going on about that? …Don't. I can't be saved. No, I shouldn't be saved. I shouldn't live."

The boy takes another step and the shadows strike his stomach, no it wasn't a strike. Sakura had managed to alter the attack once again, causing the shadows to push the boy away instead of running him through.

Sakura looked at the potentially lethal attack. "See, you saw that. This is how I am. I can't go back, and he's not going to let me go. And, even if I do go back…. I've killed a lot of people. I killed many people, killed Nii-san, killed Grandfather, and killed Nee-san! What- what do you want me to do!? I can't give back what I've taken. I've killed many people! Are you still telling me to live?!"

The girl shouts these things in confusion and sorrow, certain that there was only one way out for her. The boy understands what she means. Trapped by her crimes, she has no chance of salvation. Even if these shackles of shadows were to be broken, her own sanity, her own conscience, will destroy her. She'd forever be haunted by her own darkness.

"Of course," the boy said, with no emotion and no anger. "You took lives, so take responsibility, Sakura."

The boy grabs the holy cloth, ripping it off his arm, tearing off the only thing keeping him alive. Loosing himself, the boy continues to step forward, having something he needs to say.

"Senpai…."

"Yes, I don't know where the crime is, or how heavy it is."

Shadowy lances surge forward but merely bounce off, as blades appear on the man's body. The man grits his teeth, ignoring the pain coming from the swords.

"But I'll protect you. I'll protect you from everything. It may be hypocrisy, but ideal has always been to protect the one I love…."

More shadows strike the man, only to bounce off the swords with a spark. The man continues his advance until finally right in front of Sakura.

"No," Sakura says softly, looking at the remains of the man's body. "Senpai, your body's…."

Trace on, the man invokes in his head, concentrating the rest of his mind on a single task.

Magic circuits surged, creating prana for him to do one final spell, one final projection. He went over the spell requirements.

1\. Judging the concept of creation – completed. A ritual dagger made to assist in spells.

2\. Hypothesizing the basic structure – completed. The shape of the dagger took place in his mind.

3\. Duplicating the composition material – completed. A list of materials began filling the man's mind.

4\. Imitating the skill of its making – completed.

5\. Sympathizing with the experience of its growth – completed. Used to kill both dear friends and foreign kings. Has become an item of betrayal, a betrayal to family and a betrayal to its owner. A betrayal of magic itself.

6\. Reproducing the accumulated years - completed

7\. Excelling every manufacturing process – completed.

A dagger appears in the man's hand.

"Senpai," Sakura says.

"I'm going to punish you. This is gonna be harsh, so grit your teeth."

With a small gasp, the girl merely replies, "Yes." She holds out her chest, thinking that her senpai was going to give her the punishment she deserves.

"Let's go home, Sakura. Cut your ties from him."

The boy then stabs the dagger into Sakura, piercing her heart, within a single breath. After a flash of light, the shadows are torn apart, freeing Sakura. Sakura's hair becomes its former purple hue and her eyes also return to being purple. She's released from the shadows through the Noble Phantasm in the man's hand, Rule Breaker, a dagger meant to break mystical contracts and negate any magecraft. It shattered the connection between Sakura and Angra Mainyu, all without harming Sakura.

The man looks at the two girls, happy they're safe. Even as his memories begin fading and his mind is dying, he smiles. Tohsaka's unconscious magic was sustaining her despite its injuries and Sakura was merely unconscious.

Suddenly, the cavern shakes and the man looks to the pillar of shadows and flesh, remembering he has one last job to do. Even after losing its host, it wouldn't disappear, becoming too powerful now. With no option left, he moves to eliminate it, to finally put an end to this.

"Shirou, do you hear me?"

A soft, beautiful voice calls out to the man and he turns to see a familiar, tall woman. A goddess in human form, beautiful purple hair goes to her legs. Her eyes are covered by a blindfold and she wore a very small rag of a dress. In her hand, a spike on a chain gave off an aura of uneasiness. She was… who was she again? It's on the tip of his tongue. In any case, the man knows her. She may look dangerous and deadly but he knows she's at least trustworthy.

"Good," the man said, his mind continues to fade. "Can you take Sakura and Tohsaka and get out of here?"

"Shirou," the woman asks, concerned for not just the man, but for Sakura. "What about you?"

The man smiles. "I'll go after I destroy that thing. It'll be quick, but every second counts for Tohsaka. And Sakura would be affected by the shadow if she stays here. Angra Mainyu might be persistent and make Sakura his Master again."

The woman looks down, in solemn understanding. "Understood. I will carry Rin and Sakura. Please rest assured. I have rested enough for that."

"Please," the man said again. "Go outside with those two. The cavern's collapsing. Um. R-R-" The man tries to remember her name, but fails. His own mind is still deteriorating. "Damn. Your speed would should have no problem with the falling rocks."

The woman is silent, then speaks once again. "Then I will be going. I shall come get you after I get them to a safe place."

"Um… That's nice to hear, but make sure they're okay first," the man reminds her. "You're the only one I can trust. I'll escape by myself, so please treat Tohsaka. Sakura can't be happy without her."

Even now, after everything, the man cares more about the survival and happiness of others rather than his own safety. He's still him after all.

"Certainly, but the same goes for you, Shirou. Sakura needs you and Rin. Please remember that. …I need you to support Sakura."

The man gives a look on confusion.

"I shall hurry," the woman said, picking up Tohsaka and Sakura. "Good luck."

And with that, the woman dashes to the entrance at ridiculous agility.

Shirou Emiya then gives one final breath of relief, before turning to the pillar once again, ready to finish this once and for all.

 _Scene Break_

Sakura Matou opens her eyes to find herself in a field of flowers. Feeling no pain nor weakness, she sits up, looking around. Nothing but blue skies and flowers surrounded her, like she had been placed inside an eternal summer garden.

"I-is this heaven?" she wondered out loud, knowing she didn't deserve such a place. She put her hand in her hair to find that it had reverted back to its original brown color, the shade which was before the Makiri, before Zouken, had tainted her.

"Not quite, Tohsaka Sakura."

A voice came from the heavens and light begins to bend in front of her eyes. Soon, an image of an albino woman was standing in front of her. Her appearance looked strangely… familiar.

"Illya?" Sakura wondered. No, Illya was a child. Though this woman may look like her, she's much too old to be the young homunculus.

"That answer is not correct," the woman shakes her head. "I am merely her ancestor. Greetings, winner of the 5th Holy Grail War. I am Justeaze Lizrich von Einzbern. Congratulations on winning Heaven's Feel and obtaining the Holy Grail."

Sakura blinks in confusion. "W-what? I'm sorry, but I don't understand…."

Justeaze nods, trying to explain the situation. "Emiya Shirou has managed to destroy Angra Mainyu inside the Greater Grail, purging it. Now free, I shall use my remaining power to grant your wishes, Tohsaka Sakura. I have the energy stored in from the Fourth Holy Grail War and the Fifth Holy Grail War, along with the energy of the souls of Gilgamesh. I am able to grant three wishes."

Sakura blinked. "Wait, I still don't understand-"

"I know," Justeaze interrupts, "but unfortunately we don't have much time. Even now, my descendent approaches the Greater Grail, ready to shut down the Heaven's Feel system using the Dress of Heaven Mystic Code. I apologize for putting this pressure on you, but you must make your wish now before it's too late."

Sakura stands up, unsure of herself. "But-"

"Make your wish," Justeaze repeats.

Sakura stands there, alone. Her immediate thoughts go to her Senpai, wondering what he'd say.

 _Senpai_ , she thought.

He had sacrificed everything for her. He threw away his ideals for her, even throwing away the dream he had held in his heart since childhood. She remembers him telling her it once.

"I want to be a hero of justice."

With that thought, Sakura smiles at Justeaze, and makes her wish.

 _Scene Break_

Emiya Shirou was dying. He stared up into the dark ceiling of the collapsing cavern, then moved his head to look at his recently killed enemy. Kirei Kotomine. What an insane person. Not that he had any right to judge.

Shirou closes his eyes as his mind continues to fade, already fractured from precious harm.

Suddenly, a magic circle was drawn around him with light. With shock, Shirou looked around, desperately. He couldn't move his body, all that energy was gone, used up for his final attack on Angra Mainyu. Shirou felt his body float into the air.

"O-Onii-chan!"

A voice called out and Shirou saw a girl, wearing a strange dress, sprint desperately to him. She was I- I- He couldn't remember anymore. Those memories fades long ago.

She ran to him, but when she came to the circle, she stopped, her eyes dulling.

"Illya?" he asked confused, then realizing he knew he name again. How? Archer's arm should have been breaking down his mind. Why was he remembering things again?

"Not, quite, Emiya Shirou," Illya said, with absolutely no emotion or concern for Shirou. "I have once again take possession of Illyasviel so she cannot interfere."

"W-who are you?" Shirou demanded. He struggled once more to move, trying to escape the force keeping him down.

'Illya' merely stepped forward, beginning to levitate to get to Shirou. "I am the original homunculus used as the core of the Greater Grail, Justeaze Lizrich von Einzbern. I thank you for purging it of Angra Mainyu. His influence was… chaotic."

"T-the Greater Grail?" Shirou repeated. "But I destroyed it!"

Justeaze shakes her head. "You merely destroyed Angra Mainyu, as I said. Please try to listen."

"Why are you here?" Shirou demanded. "What do you want with me?"

Justeaze merely bowed her head. "I am here to grant the wishes of the Fifth Holy Grail War winner, Tohsaka Sakura."

Shirou can't believe what he just heard. "W-what?"

"Please try to listen. Tohsaka Sakura won the Heaven's Feel ritual. Her Rider Servant is the only one who survived in the end. And due to the fact that I have leftover prana from both the Fourth Holy Grail War Servants and Gilgamesh, who is worth several Heroic Spirits, along with the Fifth Holy Grail War Servants, I am capable of granting three wishes. Her first one, to restore the one known as Shirou Emiya."

As she speaks, Shirou's mind begins to repair and the swords covering his body begins to fade, revealing newly regrown flesh. Even his soul, which was corrupted by his own future incarnation, had been repaired, showing no signs of deterioration. However, Shirou looked at his, no Archer's arm, the arm of the Heroic Spirit EMIYA. It had begun fading from existence, blue spiritron particles emanating from it.

Justeaze notices Shirou looking at his disappearing appendage. "Unfortunately, I cannot completely restore you, as restoring your very soul took up much of the wish's energy. And the other wishes have already been made. Thus, I'm trying to conserve power by fully integrating the arm's Saint Graph directly into your soul and connecting you fully with that conceptual Weapon inside of you."

 _Saint Graph_? Shirou thought. _Conceptual Weapon_?

As far as Shirou knew, the spirit of the Holy Grail was reciting Ancient Egyptian poetry. However, Shirou felt knowledge bombard his head, memories of someone else. Archer. All sorts of knowledge went through Shirou's head, so much that it felt like his head was going to explode. He screamed as knowledge of Noble Phantasms, knowledge on weapons, knowledge on family, knowledge of friends, and knowledge of past lovers filled his head. He saw where the road of a hero of justice lead him, no Archer. And he saw the true connection between the one named Shirou Emiya and Illyasviel von Einzbern. She was-

"Unfortunately," Shirou's thoughts were interrupted by Justeaze, "I can only hope Avalon restores your arm. I'm unsure, even now. However, onto the next wish: To give Shirou Emiya the strength to fight once more. While integrating you with the arm was a start, I will also download every armament item from the Throne of Heroes itself. Enjoy."

Once again, Shirou screams from the strain of the mental intake, knowledge of more weapons fill his mind: a divine spear which slays all including gods, a shield capable of creating a world, a potion that releases one's dark side, a golden coffin which kills the unworthy who touch it, a golden key-sword that opens the Gate of Babylon, a flag capable of summoning an army of weak samurai Heroic Spirits, a sword that can annihilate anything in exchange for sacrifice, a god's hammer that summons lightning, a sash that imbues the blessings of the Greek pantheon, a wheel which represents the ideal universe ruler, ten rings which control all magecraft, a shield which is where heroes go to, and so many more. More than could be describe. It was so much, too much, threatening to overload Shirou's mind.

Once Shirou's screaming stopped, he glared at Justeaze, cursing at her. Either not understanding Shirou's pain or simply not caring, Justeaze puts her hand on Shirou's head. "And I know this won't be as much use, but I'll download my own knowledge of alchemy and anything else I can, such as the ability to speak other languages and even fragments of Third Magic. Consider this thanks."

Shirou felt the strain of the mental download once again, though this time it wasn't as painful compared to the others. He managed to let the upload happen without screaming.

"And now, the final wish," Justeaze proclaims, as Shirou ascends. "To grant Emiya Shirou's wish: to become a hero of justice. In order to do this, I shall send him to another world, where such a wish is possible."

Shirou's eyes widen upon hearing this. "No! Don't! She wouldn't want this! Let me go! Stop!"

But Justeaze just ignores his pleas, forcing him to continue his assent. Shirou continued to struggle, to try to break the magic's pull.

"No, stop! Illya! Rider! Help! Make her stop! Sakura! Sakura! SAKURA!"

A bright light fills the cavern and Shirou Emiya has left this world.

 _Scene Break_

There's nothing. Absolutely nothing. All Shirou Emiya was floating in was nothing. There was no sky, no ground, and no sea. Just nothing.

Suddenly, a burst of light and Shirou found himself emerging from… something. It felt like he was being dragged out of mud, like he could feel himself being pulled from some gunk. Barely conscious, he looks down to see space and from where he was pulled, a wall, going on and on to infinity. Shirou, in his state of mind, did not know what think of it.

Suddenly, Shirou began gaining speed, more and more until he was a comet in the sky. He was sent hurtling through space, no clear destination in sight. Suddenly, Shirou noticed something in his path, a strange tower floating in space.

 _This is going to hurt_ , Shirou thought.

Then….

CRASH!

Shirou burst through the tower, finding himself in some complex space. It was like nothing he'd ever seen, like something you'd see out of an M. C. Escher painting. Stairs were on the side, on the ceiling, in every direction: up, down, sideways, diagonal, everywhere. The areas that had no stairs was just a beautiful golden void. Soon, Shirou eventually crashed, landing on one of the platforms available.

Barely holding on, he looks up to see the shocked face of an old man.

"Got to hand it to you, kid," the old man said. "Nothing usually surprises me anymore but you really did shock me."

"H-help me," Shirou groaned before blacking out.

And that was the story of how Shirou met Kent Nelson.

 **I know, I know, not my best but please cut me some slack. I've been awake for a long time and I'm exhausted. So as of Shirou's left arm's fate, I'm gonna make a poll where you guys can decide; he can either regrow one thanks to Avalon, use a puppet arm like Shiki Ryougi's, or use an altered version of Bedivere's arm Noble Phantasm.**

 **As of, Shirou's powers in the DC Universe, without Gaia's presence weakening magecraft, Shirou's projections will now be easier to be summoned as well as not needing extra prana to continue existing. The gradation in Gradation Air is now unneeded. It will also make it possible for Shirou to establish a reality marble, but as he's never used his Unlimited Blade Works, there's a chance he never will use it. Maybe.**

 **Anyways, I'm tired so if you have any more questions, just comment of PM me. See ya, everyone! Please comment, like, and/or favorite!**


	2. Chapter 2

**Hey, everyone! I'm back and the poll results are in! I'm updating more than twice a month, must be a new record! Anyways, here are the results of the poll:**

 **For the fate of Shirou's arm:**

 **Option 1: Regrown by Avalon – 19**

 **Option 2: Bedivere's arm, the Noble Phantasm Switch On – Airgetlam - 14**

 **Option 3: Artificial like Shiki Ryougi's puppet arm or some kind of robot arm – 5**

 **Avalon wins! Yay, Avalon!**

 **Now onto the responses to the comments:**

 **To Tethriot – Due to the nature of Grail Wars, and the fact that Servants keep a copy of their memories of being summoned, it is possible EMIYA has seen a ridiculous amount of unique and different Noble Phantasms and other weaponry. I admit, this may be much, but necessary for some of the more fun Noble Phantasms.**

 **To AbyssRhythme – Thanks. I'm really happy you like my fics. I promise I'll try to live up to your expectations. Unfortunately, with the way things are progressing, Homunculi for the Tower of Fate seems unlikely.**

 **To mx2432 – He will eventually reach Reality Marble level, but not just yet. At the moment, he's not at that level.**

 **To victimsofrage – Good idea. Thank you.**

 **To – I'm afraid pseudo-Sevants like Ishtar and Parvati will not be included in this story and would like to apologize for not being able to do that or use Bedivere's Noble Phantasm arm.**

 **To superpierce – With training, his reality marble will eventually be available.**

 **To PasiveNox – A little but he has some limits. Though the DC Universe itself will make his powers stronger….**

 **To Tommy298 – Oh, he will. Just you wait.**

 **To Guest who talked about Shirou's OP state – He's not that OP but he is formidable. You'll see later in the chapters.**

 **To the Guest who talked about the fate of Shirou's missing arm – Thank you for your opinion. But you got Bedivere's arm wrong. Originally, it did eat away at the user's soul, but after the singularity, the arm stopped eating the user's soul and just gives the user all the benefits: enhanced stats and that anti-army level attack.**

 **To Hashirama 1710 – That's when in the Nasuverse. Who knows how the DC Universe, where there are less restrictions, will amplify Avalon.**

 **To hnh058513 – Yep.**

 **To jmasta32 – There are actually many Noble Phantasms that act as amplification items: Goddess of War amplifies physical abilities based on level of Mystery in the world, Rings of Solomon provide the ability to use all magecraft, etc.**

 **To DracoArtemisLeopin – Oh let's be honest, Emiya could easily have all weapons of the Throne of Heroes through the Grail War system. I just gave a reason for it.**

 **And now, let's start the fic!**

"So this boy simply fell through the void of the Tower of Fate?"

It had only been a day since the strange boy suddenly appeared in the Tower of Fate. And this teen was strange. He had Japanese features, but had natural auburn hair, a rare trait, especially for the Japanese, and golden-brown eyes. However, what was most shocking was the potent magical energy Kent could sense from the boy. The magical energy reminded Kent both of the fae and of multiple different magical artifacts. Unfortunately, the boy was also injured, missing an arm, so Kent had called his old friend Red Tornado for help.

Tornado had brought some medical equipment, and they had placed the boy

"Yes, but what's most remarkable is his arm," Kent said, watching the unconscious boy on the medical bed. "It seemed that the arm was cut off completely but it just regrew like a salamander's tail. It seems to be in perfect condition too."

"Such powerful regeneration…." Red Tornado muttered. "It's rather impressive, but it seems magical in origin. I've detected no biological nor could mechanical tampering that could cause such regeneration."

"I came to that conclusion as well," Kent said, "but kids with limb healing magic don't just fall from the sky. At least they shouldn't."

"Yes," Red Tornado agreed. "It is quite unusual. Do you think he's one of your enemies?"

Kent scratched his chin. "I don't sense any chaos magic, nor any kind of magic I'm familiar with. There are traces of familiar powers, but nothing exact."

"I see," Tornado observed. "I wonder how he ended up in the Tower. Have you consulted Nabu?"

"I swore to Inza I'd never put on that blasted helmet," Kent shook his head, "and I intend to keep that promise."

Tornado nods in understanding. "I just wish that-"

Tornado was interrupted by the stirring of the teen, which got the full attention of both android and magician.

"Are you okay?" Kent asked worriedly.

"What's your name?" Red Tornado asked.

The teen groans, siting up and grabbing his head. "W-who are y-AAAHHH!" he screamed in Japanese, opening his eyes in shock at Red Tornado.

"Is something wrong?" Red Tornado asked in Japanese.

"W-what are you?" teen said, getting over his shock.

This caused both Tornado and Kent to blink in surprise. "You don't recognize him?" Kent asked.

"Um… no…." teen replied. "Should I?"

The two looked at each other as if having a silent conversation.

"Young man," Kent said, "we will need you to tell us exactly who you are."

The teen blinked and shifted uncomfortably. "That's something… I'm not comfortable talking about…." He looks down, staring down at his hands. Then he blinked, realizing something.

"W-what?" the teen screamed, staring at his left arm in shock. "H-how…?"

The two heroes looked at each other. This boy didn't realize his powerful healing factor?

"Who are you?" Kent asked, silently casting a small truth spell. However, the teen seemed to have somehow blocked the spell, in a manner Kent was not unfamiliar.

"…Zelretch," the old man cursed under his breath, though not undetected by the boy and the android.

"My name is Emiya Shirou," the teen said carefully, looking at both heroes cautiously.

"And you're a magus," Kent concluded, causing the teen to stiffen.

"Magus?" Tornado asked, curious.

"A type of magic user from another universe that treat the mystic arts in a more scientific way," Kent explained. "I met one once, a vampire named Zelretch, who was exploring the dimensions. These magi live in a universe that restricts them, the very planets weaken their abilities."

'Gaia and Alaya,' the teen thinks. 'And Zelretch? Just who is he? I know he's some sort of magus based on that spell….'

"That's certainly interesting to know," Red Tornado said calmly.

"In any case, how could a magus somehow get here?" Kent asked the kid. "If what Zelretch told me the truth, only the Second True Magic is able to properly manipulate dimensions."

Shirou looked at Kent, eyes narrowing in suspicion.

Kent noticed this. "Please, just tell us."

"You aren't going to escape here until you do," Red Tornado further explained. "The tower won't let you."

Shirou looks around, sensing the powerful prana of the area. "Fine. You see, it all started…."

 _Scene Break_

Silence filled the room, both heroes unable to speak.

Red Tornado was the first to speak. "What a tragic past. This Holy Grail War… what a barbaric ritual…."

"But by the sounds of it… probably the real deal," Kent sighed, pinching his nose. "But in all honesty, it sounds like the cost is much too high."

"It really was…" Shirou said, remembering how the fates of Rin, Illya, Archer, and most importantly Sakura, which were changed by ritual and how many lives were both destroyed and taken by the Grail Wars.

"In any case, it seems you're stuck here," Kent said, "which means we can't simply let you go."

"So I'm a prisoner?" Shirou said, ready to fight if necessary.

"No, not at all," Red Tornado assured him. "We have several places you can go: some League areas, STAR labs-

"Or he can stay with me," Kent said, surprising both Red Tornado and Shirou.

"Kent, are you sure?" Red Tornado asked warily.

"Yes," Kent said, nodding and closing his eyes. "The kid's been through a lot and lost even more. I know what it's like to lose the person you love…. And also, I also know how it feels to essentially be thrust into a new world."

"Speaking of your time in the helmet?" Red Tornado asked.

'Helmet?' Shirou thought.

"You know me so well, old friend," Kent chuckled. "So what do you say, kid? Being sent off who knows where or becoming the ward of some random crazy stranger?"

Shirou blinked, nostalgia filling him. It… it was just like how Kiritsugu adopted him. He closed his eyes in thought, trusting his instincts. This old man seemed to be nice, and apparently, he'd be monitored despite what he chooses. Finally reaching a decision, he opened his eyes. With one motion, he pointed at Kent, with his new left hand.

Kent grinned. "Glad to hear it, kid. Can you stand?"

Shirou moves, wincing from a little pain. "I-I think so." He slides off the bed, carefully supported by Red Tornado. "Why?"

Kent's grin reminds Shirou of the Cheshire cat, mischievous and cunning, as he walks towards the door. "There's something I need you to see, something you should know."

Kent opens the door, and golden light emanates into the room. Shirou gasped as he saw what seemed to be another world, one that seemed to have its own laws of physics. Stairs and walkways filled this world, an endless golden void everywhere else.

"You see," Kent smiled, "I'm a sorcerer."

 _Two weeks later…._

It would seem Shirou had made the correct choice. Life with Kent Nelson had been ultimately peaceful, with plenty of things to do. The 'tower' was so massive, it took Shirou a while to get the layout. He could easily clean the entire tower, but it usually takes most of the morning. Kent also seemed to have enjoyed the food Shirou would always make. The old man would wolf in down, saying it was the best food he ever had. Shirou had to alter his usual recipes to make it better for the old man's health.

But what Shirou found invaluable was the amount of arcane knowledge located at the tower, along with the amount of magical artifacts. Kent had a treasure trove of mystical powers that could be comparable to the Gate of Babylon itself. It had plenty of knowledge, though the information Shirou sought after was rare, even with these resources.

"Sakura…" Shirou said, "I'm coming back to you."

 **And done! I hope you all like this. And no, Shirou will not be going back to his dimension this early. Maybe later, much later. Anyways, I hope you all enjoy. Please Follow, Favorite, and Comment and stuff. Until next time!**


	3. Chapter 3

**Hello, my dear readers! It's been a while! I'm sorry for not updating sooner but I've been preoccupied by testing and such. However, with this week being the end of the school year, I'm free! Now let's start responding to comments:**

 **To hnh058513 – I saw. Pretty awesome lore drop.**

 **To micelzod – I did not write any Servants into this, at least for now. Additionally, Unlimited Blade Works will typically be used in times of emergency, though he'll need to practice with it a bit before it's ready.**

 **To superpierce – Sorry. I'll try to extend the next few chapters.**

 **To – I'll take that into account.**

 **To longbowchris50 – No, he only loses Avalon in the Fate route. In Unlimited Blade Work route and Heaven's Feel Route, Avalon remains undiscovered.**

 **To AriFrost – I have plans for Sakura, Rin, and Medusa, though that is for long in the future.**

 **To shadyxlr – I usually don't like giving spoilers but Sakura will not be appearing in this story for a while.**

 **To YukiNonShita – True, but the prana cost will definitely make it more of a last resort weapon.**

 **To alexkellar – Well, they couldn't just let a combat-specializing mage go into an unknown world. In a world of villains, precaution is necessary. And acting as a ward to Kent Nelson is beneficial to Shirou, as the old man has all sorts of relics and magical tomes that could be of assistance to Shirou.**

 **To Dragonskyt – A little. I got most of the transcripts and descriptions of those events, but I attempted to modify it to better show what happened and the important things. Also, sorry if I got my intel wrong.**

 **To DarksZeroFenix0 – I'm flattered.**

 **To doubledamm – Yeah, he is and due to him never encountering Gilgamesh during the Heaven's Feel route, he won't have much qualms on using it. Though again, like with the Rings of Solomon, he'll have to be careful when using it for fear of wasting prana.**

 **To Jose19 – He will get a new life, but still pine over Sakura.**

 **To the Guest that posted on February 9 – Thank you. I hope you enjoy the rest of the story.**

 **Now time to start this story.**

It's been three months since Shirou first became Kent Nelson's ward. Kent was a kind and wise guardian, providing Shirou with all the freedom and resources available. Shirou had surprisingly discovered that the Tower of Fate that he and Kent lived in was located in Salem, Massachusetts in the United States. Luckily Shirou lived with an English teacher. Good old Fuji-nee.

Shirou had managed to acclimate to this new world at a slow but steady pace. Both the current year and the technological level is higher than his own world's and the aliens of this world weren't superbeings like the Types. Instead, the aliens were similar to human beings in certain aspects, though they typically have some sort of strange feature or power. Additionally, there are an increased number of countries that did not exist in Shirou's old world. However, what Shirou found most surprising was the concept of superheroes; they were an actual thing in this world, with both humans and aliens, dressed in costumes, fought against crime.

As for Shirou's magical studies, he discovered the thaumaturgic systems of this world were so simple, yet so incredible. It was as if this world was still in an Age of Gods, though with the levels of magecraft Shirou's seen, that may be true. Even a novice like Shirou could make use of some miracles. He found spells and rituals for all sorts of purposes, though none for navigating through dimensions. As unfortunate as it is, Shirou found no way to get back to Sakura, at least for now.

Having heard of Shirou's dilemma, Kent has been going on journeys around the world, in search of the mystical. He would leave in the morning, but he'd always return by the time Shirou started dinner. However, one day, Kent didn't make it to their usual family dinners, then missing the next one and the next one. Soon, Kent had been missing for 23 days, causing both Shirou and Red Tornado to worry.

"And you're saying that this Madame Xanadu had no information?" Red Tornado said over the communication device.

"I'm afraid not," Shirou sighed. "I visited her and she had some mystical talent, though she herself seemed to be a nonbeliever. She did say something about a tall, muscular man with a goatee grabbing Kent and disappearing. It scarred her pretty badly."

"We'll send someone to check her out and provide some compensation," Red Tornado replied. "And Kent's cane?"

"It appeared inside the Tower at the time of Kent's disappearance. I placed it someplace safe."

"That's good to know. I shall be sending a team over to check up on you, Shirou. They're that covert team that the League has been utilizing."

"The one made of former sidekicks?" Shirou asked.

"It would be better for you not to call them that. They're rather sensitive to that word."

Shirou laughs. "I understand. I'll make sure-"

The sounds of bells chime, filling the room and causing Shirou to grow quiet.

"Someone's entered the tower," he reported. "Your team?"

"Most likely," Tornado said. "Please go greet them."

Shirou closes his eyes, letting the spells tell him of their location. "They seem to be in the location where I placed Kent's cane. We'll talk later, Tornado."

"Understood," Red Tornado nodded as he switched off the communication device. Shirou, meanwhile, headed to the door, bringing out a ring full of keys. These keys were enchanted by Kent to help Shirou get around the tower more easily. He put a key with a snowflake's emblem on it into the keyhole, twisting the doorknob and opening the door, now a portal. It took him to a frozen wasteland where three people shivered in the cold: a handsome, black haired, muscular Caucasian boy with permanent scowl, a green skinned girl with red hair, and a dark skinned, blonde boy with strange tattoos. When they saw him, they seemed to get ready for a fight, causing Shirou to draw his blades in retaliation.

"Who are you?" Shirou asked .

"We could be asking you the same thing," the tattooed boy asked.

"Shirou Emiya," Shirou said, still not putting his blades away.

"I'm Aqualad, he's Superboy, and that's Miss Martian," the tattooed boy replied.

 _The sidekicks of the Justice League, I take it,_ Shirou thought. _Still, I'll have to make sure…._

"And who exactly sent you?"

"Red Tornado," Miss Martian explained, before taking out Red Tornado's key to the tower. Shirou lowered his weapons.

"I see," Shirou said as his weapons dissolved into light. "I apologize, but I had to make sure."

"We understand," Aqualad nods, raising a hand to tell his friends to stand down.

Shirou looked around. "Where's the cane? I was using this place to keep it safe."

"Some of our companions grabbed it and it teleported them off somewhere," Aqualad said.

"W-what?" Shirou blinked. "It shouldn't teleport unless…." Shirou's eyes narrowed. "Follow me. I don't think you guys are the only people visiting the tower."

He leads them through the door he originally came from.

"Ugh. This magic stuff is giving me a headache," Superboy complained.

"It's a little disorienting at first," Shirou shrugged in agreement, "but you get used to it."

"I find it amazing," Miss Martian gaped at her surroundings.

"Thanks, Miss Martian," Shirou smiled.

"Oh, you can just call me Megan," Miss Martian said.

"And you can call me Kaldur, Shirou," Aqualad said.

Shirou turns to Superboy. "And you?"

Superboy just responds with silence.

"He's just goes by Superboy," Megan explained.

"Well, Superboy, Kaldur, and Megan, please dry off near the fireplace," Shirou said. "I'll try to locate your friends."

The three heroes nod as they shake the snow off of their bodies, warming by the fireplace. Shirou summons the Orb of Nabu, a scrying tool used by Doctor Fate. He detected to sources of magical energy in the tower, one being extremely powerful and chaotic, the other being calm, average, and orderly.

"I think I found them," Shirou said, taking out another key. The trio following, Shirou opens a new door, a portal filled with golden light appearing. They step right through, and instantly, all four of them fall to the ground below.

"Ooo," a cocky voice comes from beside them. "That's got to smart."

"Knock it off, Wally," a female voice snapped.

Shirou looked up to see a blonde Asian-Caucasian girl and a red headed boy standing before them, with Kent standing behind them.

"Kent!" Shirou beamed, getting to his feet and hugging his guardian. "You're alive."

"I don't go down so easily," Kent smiled before looking at the still recovering Kaldur, Superboy, and Megan. "Friends of yours?"

Suddenly, blasts of crimson energy and lightning rained down from above. Shirou reacted instinctively, summoning Rho Aias to protect them.

"Friends of yours?" Shirou quipped.

The heroes instantly got into battle positions, the blonde aiming her bow, Kaldur drawing his water blades, Megan levitated, and Superboy getting into a defensive stance.

"Wally," Kaldur barked, "go with Nelson! We'll hold them back."

Shirou and Kent went to the bell, as Kent smacked the bell with his cane. Shirou, Wally, and Kent quickly ran into the bell, being transported to the top of the tower, an area protected with all manner of spells and wards. In the center of the tower floated a golden helmet. Kent raised a hand to grab it when a blast of crimson cut right through him. Kent flew back, blood spattering.

"Kent!" Shirou cried, catching him and glaring at the source. A short demonic-looking boy stood there, his hand glowing with crimson energy and a monstrous cat purring by his side.

"Is he going to be okay?" Wally said.

Shirou turned to Wally. "Take him. I'll take care of them."

Giving the injured Kent to Wally, Shirou stepped up and approached the boy, using a chain to grab the helmet.

"You!" the boy hissed. "I want that helmet! Give it here!"

"Klarion right?" Shirou said, remembering him from one of Kent's books. "Come get it."

Shirou threw the helmet back towards Wally and Kent as Shirou summons Kanshou and Bakuya. Klarion sneered as he released bolts of energy at Shirou, who deflected them instantly. Klarion sneered in surprise.

"What?!" he roared, releasing more blasts. Shirou merely deflected the blasts once again as he charged Klarion, ducking in and slashing at him. The cat roared to protect his master but Shirou kicked it away.

"Yikes!" Klarion squeaked, using a shield to guard him. He jumped back, breathing fire down on to Shirou, who backflipped away.

Klarion suddenly turned into smoke, heading straight towards Wally and Kent but falling blades blocked his path. Klarion materialized but jumped away to dodge a falling Shirou, who attempted to impale him with a spear.

"You're really pissing me off, jerk!" Klarion said, snapping his fingers. Instantly, the sword wall morphed and becoming pythons that struck at Shirou.

Shirou dodged the first snake before beheading the other. He jumped over a third and ran over its body to continue his assault on Klarion.

"TEEKL!" Klarion shouted and the cat jumped, morphing and becoming humanoid in the process. It slashed at Shirou with its claws, causing him to jump back. However, the sword-snakes surrounded him, attempting to strike at him.

"Damn it!" Shirou said, managing to impale another snake with a spear. However, more foes swarmed around him.

Klarion grinned viciously, turning to the metahuman and the fallen sorcerer. "Now for that helme-"

Klarion's victory was caught short when he saw Wally put on the helmet.

"NO!" Klarion roared, aiming red hot flames charge towards them, only for the flames to part by golden light. The light burned enemies, blasting the sword snakes back and causing the cat to hiss. Shirou covered his eyes as the light shone, sensing a vast amount of power build up.

As the light faded, Shirou saw a man dressed in blue, adorned in golden armor, a golden cape, and a golden helmet. Shirou recognized the apparel from some of Kent's old photos. This was Doctor Fate, the Lord of Order.

"Klarion," Fate decreed, his voice echoing in authority and strength. "Leave this place. Now."

"Nabu!" Klarion growled. "I don't take orders from you, you old fart!"

"Then your fate," Doctor Fate says, raising his hand, "has been sealed."

Fate moved his hand and beams of light fire into the air, collecting into a sphere. The sphere then began raining down light on the area. Both Shirou and Teekl dodged for cover as Klarion turned to ravens, which narrowly dodge the blasts. Fate and Shirou charge Klarion, spells and swords in their respective hand.

Klarion raised his hand as a whirlwind surrounds the entire area, causing them all to go airborne. Stones and bricks flew, causing debris to strike the two mages. In defense, Doctor Fate put up a spherical golden barrier, to guard against physical attacks while Shirou went into a defensive stance, reinforcing his body.

"You're weak, Nabu!" Klarion laughed. "Out of practice and that boy has zero affinity for the mystic arts! And that other mage seems to be having trouble!"

"We are not as incapable as you think!" Fate glared, releasing a golden blast at Klarion.

The witch-boy laughs as his shield blocks the blast. However, a crimson spear flies through his shield as if nothing was there, piercing Klarion's shoulder. Klarion roars in pain as he rips the spear out, his whirlwind spell fading. Fate releases another blast of energy at the incapacitated Klarion but the witch-boy's familiar gets him out of the way.

"Meow," the cat snapped.

"I'm not running," Klarion gritted his teeth, as his wounds slowly healed. "I can beat them."

"Don't be a fool, brat," Fate said, as he helped Shirou get to the ground safely. "This is a battle you cannot win."

"Don't tell me what I can't do!" Klarion slammed his hands on the ground, circles of hellfire summoning demons. The battalion of hell surrounded them, hissing and growling. "Sic 'em."

The demons charged at them, causing Fate to levitate high and fire beams of golden light at demons. Shirou stayed on the ground, hacking at demons with twin swords. However, for each they kill, two more take their place.

"There's no end to them!" Fate growled in frustration.

"Give me some room!" Shirou ordered. Fate nodded as a barrier wrapped around Shirou, keeping the surrounding demons from attacking. Shirou raised his hand as he summons a single war horn. "La Black Luna!"

The horn transforms, wrapping around Shirou and morphing into a large musical instrument. Shirou blows the horn, a powerful soundwave bursts from all directions, shattering the barrier around him and annihilating every demon in the area. The only surivors were Fate, Klarion, and his cat, who was shielded alongside Klarion.

"No, no, no!" Klarion roared, stomping his feet. "You cheated!"

"Enough!" Fate said, aiming a blast at the two.

Klarion instantly raised his shield but the blast parted, homing in on Teekl, blasting the cat back. The cat landed on its side, transforming back into its housecat form.

"Teekl!" Klarion said, heading to the side of his familiar. He glared at the Lord of Order. "You dare attack the defenseless pussycat!"

"We both know that isn't a mere cat, Klarion," Fate scolds as Klarion seems to fade in and out from existence. "It is difficult for both Lords of Order and Chaos to exist on this plane. Just as I am bound to the helmet, you are bound here by a different manner."

"Good to know," Shirou said, raining swords down on the pair, but Klarion managed to recover.

"Holy crap!" he shouted, teleporting to evade the swords. He and Teekl appear a few meters away, where both are hit by Fate's blast. They land on their side, stumbling up. "L-let's get out of here!"

As Klarion prepares to teleports away, he sees Shirou, bow in hand and a giant thin screw in the other. Power emanated from Shirou, promising death and destruction. For the first time in many years, Klarion felt a shadow of fear.

"Caladbolg," Shirou intoned, releasing the arrow. Klarion screamed, shielding his cat as he teleported away. However, the twisted space left some degrees of damage on the Lord of Chaos, damaging him greatly as he made his escape.

Shirou panted in rage. "I-is he dead?"

"No, Klarion is chaos personified," Fate said, as he dropped to his feet. "That attack did damage him, but both his anchor and his life survived."

Shirou fell to the ground, exhausted, his weapons fading away. He punched the ground angrily. "Damn it."

He looked to Kent, not moving on the ground nearby. Fate had placed a barrier shortly before their fight. Shirou stumbled to Kent, blood no longer flowing from his wound. His reinforced hearing heard no blood pumped, no heartbeat. Shirou fell to the ground. He failed someone close to him again. Kent Nelson, his guardian, was dead.

"Kent," Shirou sobbed, "I-I'm so sorry."

Tears fell on the corpse, as remorse and regret filled Shirou. He couldn't save him. He couldn't protect the person who took him in and helped in. Why? Why couldn't he save anyone he cares about?

"He's okay."

A small voice broke Shirou from his trance. He turned to see the boy from before, Wally West, wearing a sad look as he held the Helmet of Fate.

"W-what?"

"Kent. He told me… he'll be okay," Wally said. "He told me to tell you not to worry. This isn't your fault and he doesn't blame you for any of it."

"He should," Shirou snapped, causing Wally to flinch.

"It's not," Wally stated, as if it was a fact. "You couldn't have seen that blast coming. You couldn't have stopped it. He doesn't want you to blame yourself."

Wally walked closer to Shirou, outstretching his hand. "C'mon. Let's get you cleaned up."

Weakly and timidly, Shirou took the boy's hand.

 _Scene Break_

The funeral was lovely. By the grave of his wife Inza, the body of Kent Nelson descended, surrounded by his friends. Members of the Justice Society, old friends from the Justice League, the young heroes that traveled to save him, and his ward Shirou, they all said their words about Kent. He was a hero, a great man, and a friend.

"Shirou," a man covered in a bat-like cowl, the Batman, approached him. "We'd like you to join the Team."

"Don't you think this is too soon," Tornado advised. "He just lost-"

"I'm fine," Shirou said with certainty. "And I want to join the team. I think… I think Kent would have wanted this."

Batman nodded, shaking the young mage's hand. "We'll have a room prepared for you back at base."

The teenagers surrounded him, patting him on the back.

"Welcome to the team," Wally said.

"It'll be nice to have another magic user," Kaldur smiled.

"And you can show us a move or two," a new boy, Robin, said.

"Yeah, what they said," the blonde archer, Artemis, nodded.

Shirou gave a small smile as he followed them to a local Zeta tube, a teleporter. In a flash of light, Shirou found himself inside a new area, an underground cavern with high tech technology integrated into it. Shirou gave a small sigh.

"Well, I guess this is home now," he said sadly.

Megan frowned, taking his hand. She and the others gave him warm smiles. "C'mon. Let's give you the tour."

Shirou blinked before returning a smile, and went with his new team, his new family, to explore their new home.

 _Scene Break_

Klarion gasped as he fell into a dark room, Teekl jumping away unharmed. The cat quickly jumped on a keyboard, surrounding monitors lighting up before it went to Klarion, licking his wounds. Klarion's lower torso was ripped apart, his left arm burned to a crisp. White silhouettes appeared on the monitors.

"Klarion," a surprised voice came from one of the silhouettes. "What happened?"

Klarion bit his tongue as pain roared throughout his body. He cursed Nabu, he cursed those teen heroes, and most of all, he cursed that bastard red head sword mage. His body slowly regenerated and he crawled to his feet.

"Klarion?" another voice asked.

"I'm fine," he spat, rage emanating from his body. "We have a problem."

 **And done. Not bad if I do say so myself. I'm a bit exhausted but I hope you all enjoyed this chapter and I hope you all like this integration into the Young Justice series. I know most usually have the crossover either come during the beginning of the series but I wanted to try something new.**

 **Anyways, before I pass out, please favorite, follow, and/or comment! I really want to see what you all think about my writing. Once again, I hope you all enjoy this new chapter and this is Mythmaker258 signing off.**

 **Oh. P.S. Please send a comment if you have a good idea on what Shirou's superhero name should be, because I always have difficulties thinking of something for him.**


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